AMBER Archive (2007)

Subject: AMBER: prep file new residue

From: Dr M. Blomberg (mb635_at_cam.ac.uk)
Date: Mon Apr 23 2007 - 03:48:27 CDT

Hi,

I want to do simulatons with Glutathione as a substrate, which is a
tripeptide (QCG) with the Glu forming the peptide bond with it's sidechain
carboxylic group.

I have tried to change the connectivity tree, i.e. M, B, E etc, and
creating a new residue prep file with the main chain going through the side
chain. However, when I load the prep file into leap I get the error below
and the new residue is not loaded. Could someone please tell me how to do
this correctly?

Thanks,

Mattias Blomberg

Loading Prep file: ./glg.in
65 pairs of atoms within potential bonding distance
45 are not H-H pairs
Atom .R<1 1>.A<CB 7> has maximum number of bonds.
Atom .R<1 1>.A<CA 5> has maximum number of bonds.
Atom .R<1 1>.A<CA 5> has maximum number of bonds.
.
.
.

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